Single cell UOW

Pixel and cell QC report plus Leiden Clustering

Project description: Initial datasets shared by Australian collaborators (Tassiani Sarretto, Helena Anastacio). Three conditions (stem cells, cells grown for 7 and 14 days). 12 replicates per condition.

Date: 2023-05-30

Config: /Users/alberto-mac/Documents/DA_ESPORTARE/LOCAL_EMBL_FILES/g_shared/shared/alberto/projects/spacem-reports/australia-project/initial_reports/config_full_v2.yml

Notebook version: v0.2.0.post3+g966cb55.d20230408 (git-commit: 9f02807)

Report parameters

  • Biological key: growthConditions
  • Slide key: slide
  • Process slides independently: False
  • Replicate key: replicate_nb_overall
  • Masking key: None
  • AnnData pattern: /Users/alberto-mac/Documents/DA_ESPORTARE/LOCAL_EMBL_FILES/g_shared/shared/alberto/projects/spacem-reports/australia-project/initial_reports/anndatas/{slide}-well{well}-{row}{col}.h5ad
  • AnnData type: AnnDatas downloaded from Metaspace
  • Metadata file path: /Users/alberto-mac/Documents/DA_ESPORTARE/LOCAL_EMBL_FILES/g_shared/shared/alberto/projects/spacem-reports/australia-project/initial_reports/metadata_mod_full.csv

Table of Content

  1. Replicate coverage
  2. List of datasets
  3. All Slides

Replicate coverage

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List of datasets

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  datasetName datasetId growthConditions slide row col replicate_nb_overall group submitter PI organism organismPart condition mask_day_0 mask_day_7 mask_day_14 well ionisationSource maldiMatrix analyzer resPower400 polarity uploadDateTime FDR@10% database opticalImage dataset_name slide_batch_key replicate_nb_per_slide_0 replicate_nb_overall_0 replicate_nb_per_slide_7 replicate_nb_overall_7 replicate_nb_per_slide auto_generated_dataset_name mask_slide_TS36
0 TS37 well9 - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA 2023-02-01_06h56m45s 14 days TS37 C 2 1 nan Tassiani Sarretto Shane Ellis cultured cells Skin control True True False 9 MALDI DHA Orbitrap 120000 positive 2023-02-01T06:56:45.358 23 HMDB - v4 No optical image TS37-well9-C2 1 nan nan nan nan 1 TS37-C2 False
1 TS37 well8 top left - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA 2023-02-01_06h55m41s 14 days TS37 B 2 2 nan Tassiani Sarretto Shane Ellis cultured cells Skin control True True False 8 MALDI DHA Orbitrap 120000 positive 2023-02-01T06:55:41.764 127 KEGG - v1 No optical image TS37-well8-B2 1 nan nan nan nan 2 TS37-B2 False
2 TS37 well7 bottom left - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA 2023-02-01_06h54m38s 14 days TS37 A 2 3 nan Tassiani Sarretto Shane Ellis cultured cells Skin control True True False 7 MALDI DHA Orbitrap 120000 positive 2023-02-01T06:54:39.019 405 HMDB - v4 No optical image TS37-well7-A2 1 nan nan nan nan 3 TS37-A2 False
3 TS37 well3 middle right - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA 2023-02-01_06h54m03s 14 days TS37 C 1 4 nan Tassiani Sarretto Shane Ellis cultured cells Skin control True True False 3 MALDI DHA Orbitrap 120000 positive 2023-02-01T06:54:03.789 120 HMDB - v4 No optical image TS37-well3-C1 1 nan nan nan nan 4 TS37-C1 False
4 TS37 well2 bottom right - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA 2023-02-01_06h53m25s 14 days TS37 B 1 5 nan Tassiani Sarretto Shane Ellis cultured cells Skin control True True False 2 MALDI DHA Orbitrap 120000 positive 2023-02-01T06:53:25.910 227 HMDB - v4 No optical image TS37-well2-B1 1 nan nan nan nan 5 TS37-B1 False
5 TS37 well1 bottom left - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA 2023-02-01_06h52m46s 14 days TS37 A 1 6 nan Tassiani Sarretto Shane Ellis cultured cells Skin control True True False 1 MALDI DHA Orbitrap 120000 positive 2023-02-01T06:52:46.833 3 KEGG - v1 No optical image TS37-well1-A1 1 nan nan nan nan 6 TS37-A1 False
6 TS38 well9 - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA 2023-02-01_06h24m02s 14 days TS38 C 2 7 nan Tassiani Sarretto Shane Ellis cultured cells Skin control True True False 9 MALDI DHA Orbitrap 120000 positive 2023-02-01T06:24:02.680 355 KEGG - v1 No optical image TS38-well9-C2 2 nan nan nan nan 1 TS38-C2 False
7 TS38 well1 - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA 2023-02-01_06h17m43s 14 days TS38 A 1 8 nan Tassiani Sarretto Shane Ellis cultured cells Skin control True True False 1 MALDI DHA Orbitrap 120000 positive 2023-02-01T06:17:43.298 312 HMDB - v4 No optical image TS38-well1-A1 2 nan nan nan nan 2 TS38-A1 False
8 TS38 well7- Fixed neuronal cells, 30um, positive ion mode, sublimation DHA 2023-02-01_06h22m51s 14 days TS38 A 2 9 nan Tassiani Sarretto Shane Ellis cultured cells Skin control True True False 7 MALDI DHA Orbitrap 120000 positive 2023-02-01T06:22:51.341 180 HMDB - v4 No optical image TS38-well7-A2 2 nan nan nan nan 3 TS38-A2 False
9 TS38 well2 - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA 2023-02-01_06h19m54s 14 days TS38 B 1 10 nan Tassiani Sarretto Shane Ellis cultured cells Skin control True True False 2 MALDI DHA Orbitrap 120000 positive 2023-02-01T06:19:54.395 296 KEGG - v1 No optical image TS38-well2-B1 2 nan nan nan nan 4 TS38-B1 False
10 TS38 well3 - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA 2023-02-01_06h21m37s 14 days TS38 C 1 11 nan Tassiani Sarretto Shane Ellis cultured cells Skin control True True False 3 MALDI DHA Orbitrap 120000 positive 2023-02-01T06:21:37.336 117 KEGG - v1 No optical image TS38-well3-C1 2 nan nan nan nan 5 TS38-C1 False
11 TS35 well8 - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA 2023-02-01_05h15m20s 7 days TS35 B 2 1 nan Tassiani Sarretto Shane Ellis cultured cells Skin control True False True 8 MALDI DHA Orbitrap 120000 positive 2023-02-01T05:15:20.200 64 HMDB - v4 No optical image TS35-well8-B2 1 nan nan 1.000000 1.000000 1 TS35-B2 False
12 TS35 well9 - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA 2023-02-01_05h17m05s 7 days TS35 C 2 2 nan Tassiani Sarretto Shane Ellis cultured cells Skin control True False True 9 MALDI DHA Orbitrap 120000 positive 2023-02-01T05:17:06.036 46 HMDB - v4 No optical image TS35-well9-C2 1 nan nan 2.000000 2.000000 2 TS35-C2 False
13 TS35 well3 - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA 2023-02-01_05h10m32s 7 days TS35 C 1 3 nan Tassiani Sarretto Shane Ellis cultured cells Skin control True False True 3 MALDI DHA Orbitrap 120000 positive 2023-02-01T05:10:32.445 274 HMDB - v4 No optical image TS35-well3-C1 1 nan nan 3.000000 3.000000 3 TS35-C1 False
14 TS35 well7 - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA 2023-02-01_05h11m11s 7 days TS35 A 2 4 nan Tassiani Sarretto Shane Ellis cultured cells Skin control True False True 7 MALDI DHA Orbitrap 120000 positive 2023-02-01T05:11:11.516 43 HMDB - v4 No optical image TS35-well7-A2 1 nan nan 4.000000 4.000000 4 TS35-A2 False
15 TS35 well2 - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA 2023-02-01_05h09m40s 7 days TS35 B 1 5 nan Tassiani Sarretto Shane Ellis cultured cells Skin control True False True 2 MALDI DHA Orbitrap 120000 positive 2023-02-01T05:09:40.107 138 HMDB - v4 No optical image TS35-well2-B1 1 nan nan 5.000000 5.000000 5 TS35-B1 False
16 TS35 well1 - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA 2023-02-01_05h08m38s 7 days TS35 A 1 6 nan Tassiani Sarretto Shane Ellis cultured cells Skin control True False True 1 MALDI DHA Orbitrap 120000 positive 2023-02-01T05:08:38.102 66 HMDB - v4 No optical image TS35-well1-A1 1 nan nan 6.000000 6.000000 6 TS35-A1 False
17 TS36 well8 - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA 2023-02-02_01h43m22s 7 days TS36 B 2 7 nan Tassiani Sarretto Shane Ellis cultured cells Skin control True False True 8 MALDI DHA Orbitrap 120000 positive 2023-02-02T01:43:22.810 52 HMDB - v4 No optical image TS36-well8-B2 2 nan nan 1.000000 7.000000 1 TS36-B2 True
18 TS36 well7- Fixed neuronal cells, 30um, positive ion mode, sublimation DHA 2023-02-02_01h42m25s 7 days TS36 A 2 8 nan Tassiani Sarretto Shane Ellis cultured cells Skin control True False True 7 MALDI DHA Orbitrap 120000 positive 2023-02-02T01:42:25.784 264 KEGG - v1 No optical image TS36-well7-A2 2 nan nan 2.000000 8.000000 2 TS36-A2 True
19 TS36 well3 - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA 2023-02-02_01h41m39s 7 days TS36 C 1 9 nan Tassiani Sarretto Shane Ellis cultured cells Skin control True False True 3 MALDI DHA Orbitrap 120000 positive 2023-02-02T01:41:39.335 136 KEGG - v1 No optical image TS36-well3-C1 2 nan nan 3.000000 9.000000 3 TS36-C1 True
20 TS36 well1 -Fixed neuronal cells, 30um, positive ion mode, sublimation DHA 2023-02-02_01h40m13s 7 days TS36 A 1 10 nan Tassiani Sarretto Shane Ellis cultured cells Skin control True False True 1 MALDI DHA Orbitrap 120000 positive 2023-02-02T01:40:13.578 252 HMDB - v4 No optical image TS36-well1-A1 2 nan nan 4.000000 10.000000 4 TS36-A1 True
21 TS36 well2 - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA 2023-02-02_01h40m56s 7 days TS36 B 1 11 nan Tassiani Sarretto Shane Ellis cultured cells Skin control True False True 2 MALDI DHA Orbitrap 120000 positive 2023-02-02T01:40:56.194 133 HMDB - v4 No optical image TS36-well2-B1 2 nan nan 5.000000 11.000000 5 TS36-B1 True
22 TS36 well9 - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA 2023-02-01_05h43m12s 7 days TS36 C 2 12 nan Tassiani Sarretto Shane Ellis cultured cells Skin control True False True 9 MALDI DHA Orbitrap 120000 positive 2023-02-01T05:43:12.895 127 KEGG - v1 No optical image TS36-well9-C2 2 nan nan 6.000000 12.000000 6 TS36-C2 True
23 TS33 well8 - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA 2023-02-01_02h14m46s Stem cells TS33 B 2 1 nan Tassiani Sarretto Shane Ellis cultured cells neuron control False True True 8 MALDI DHA Orbitrap 120000 positive 2023-02-01T02:14:46.823 228 HMDB - v4 No optical image TS33-well8-B2 1 1.000000 1.000000 nan nan 1 TS33-B2 False
24 TS33 well9 - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA 2023-02-01_02h15m58s Stem cells TS33 C 2 2 nan Tassiani Sarretto Shane Ellis cultured cells Skin control False True True 9 MALDI DHA Orbitrap 120000 positive 2023-02-01T02:15:58.683 122 HMDB - v4 No optical image TS33-well9-C2 1 2.000000 2.000000 nan nan 2 TS33-C2 False
25 TS33 well7 - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA 2023-02-01_02h14m02s Stem cells TS33 A 2 3 nan Tassiani Sarretto Shane Ellis cultured cells neuron control False True True 7 MALDI DHA Orbitrap 120000 positive 2023-02-01T02:14:02.055 147 HMDB - v4 No optical image TS33-well7-A2 1 3.000000 3.000000 nan nan 3 TS33-A2 False
26 TS33 well3 -Fixed neuronal cells, 30um, positive ion mode, sublimation DHA 2023-02-01_02h13m08s Stem cells TS33 C 1 4 nan Tassiani Sarretto Shane Ellis cultured cells neuron control False True True 3 MALDI DHA Orbitrap 120000 positive 2023-02-01T02:13:08.967 32 HMDB - v4 No optical image TS33-well3-C1 1 4.000000 4.000000 nan nan 4 TS33-C1 False
27 TS33 well2 2023-02-01_02h11m55s Stem cells TS33 B 1 5 nan Tassiani Sarretto Shane Ellis cultured cells neuron control False True True 2 MALDI DHA Orbitrap 120000 positive 2023-02-01T02:11:55.197 55 HMDB - v4 No optical image TS33-well2-B1 1 5.000000 5.000000 nan nan 5 TS33-B1 False
28 TS33 well1 2023-02-01_02h06m42s Stem cells TS33 A 1 6 nan Tassiani Sarretto Shane Ellis cultured cells neuron control False True True 1 MALDI DHA Orbitrap 120000 positive 2023-02-01T02:06:42.827 193 HMDB - v4 No optical image TS33-well1-A1 1 6.000000 6.000000 nan nan 6 TS33-A1 False
29 TS34 well9 - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA 2023-02-01_02h56m42s Stem cells TS34 C 2 7 nan Tassiani Sarretto Shane Ellis cultured cells Skin control False True True 9 MALDI DHA Orbitrap 120000 positive 2023-02-01T02:56:42.389 49 HMDB - v4 No optical image TS34-well9-C2 2 1.000000 7.000000 nan nan 1 TS34-C2 False
30 TS34 well8 - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA 2023-02-01_02h44m11s Stem cells TS34 B 2 8 nan Tassiani Sarretto Shane Ellis cultured cells Skin control False True True 8 MALDI DHA Orbitrap 120000 positive 2023-02-01T02:44:11.325 40 KEGG - v1 No optical image TS34-well8-B2 2 2.000000 8.000000 nan nan 2 TS34-B2 False
31 TS34 well7 - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA 2023-02-01_02h43m29s Stem cells TS34 A 2 9 nan Tassiani Sarretto Shane Ellis cultured cells Skin control False True True 7 MALDI DHA Orbitrap 120000 positive 2023-02-01T02:43:29.710 46 HMDB - v4 No optical image TS34-well7-A2 2 3.000000 9.000000 nan nan 3 TS34-A2 False
32 TS34 well3_2 - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA 2023-02-01_02h41m43s Stem cells TS34 C 1 10 nan Tassiani Sarretto Shane Ellis cultured cells Skin control False True True 3 MALDI DHA Orbitrap 120000 positive 2023-02-01T02:41:43.387 94 HMDB - v4 No optical image TS34-well3-C1 2 4.000000 10.000000 nan nan 4 TS34-C1 False
33 TS34 well2 - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA 2023-02-01_02h39m48s Stem cells TS34 B 1 11 nan Tassiani Sarretto Shane Ellis cultured cells Skin control False True True 2 MALDI DHA Orbitrap 120000 positive 2023-02-01T02:39:48.661 78 HMDB - v4 No optical image TS34-well2-B1 2 5.000000 11.000000 nan nan 5 TS34-B1 False
34 TS34 well1 - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA 2023-02-01_02h39m05s Stem cells TS34 A 1 12 nan Tassiani Sarretto Shane Ellis cultured cells Skin control False True True 1 MALDI DHA Orbitrap 120000 positive 2023-02-01T02:39:06.024 131 HMDB - v4 No optical image TS34-well1-A1 2 6.000000 12.000000 nan nan 6 TS34-A1 False

All Slides

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Well layout (Slide TS33)

Well layout (Slide TS34)

Well layout (Slide TS35)

Well layout (Slide TS36)

Well layout (Slide TS37)

Well layout (Slide TS38)

Number of Annotations and Pixels in AnnDatas files (All Slides)

  # pixels # annotations Comments/Suggestions
After loading datasets in 'All Slides' jointly 196311 80 When few annotations are found at this stage, consider creating a custom Metaspace database
After selecting intra-cellular pixels 58912 80 If few pixels are left at this stage, you may need to adjust the `selection_metabolites` and `selection_threshold` parameters, and then download AnnDatas files again from Metaspace. See download summary report for more details about these parameters.
After filtering annotations found in less than 200 pixels and pixels with less than 20 annotations 52722 80 If not many pixels and/or annotations are left at this stage, you may need to adjust the parameters `min_pixels_per_annotation` and `min_annotations_per_pixel`

Annotations/Pixels Statistics (All Slides)

PCA (All Slides)

UMAP (All Slides)

Potential variance in UMAP associated with x/y position of well on slide

Potential variance in UMAP associated with slide number (independent on condition)

Distance between datasets (All Slides)

Intra-label vs. inter-label distance (All Slides)

Circle size and number inside circles correspond to euclidean distance $D_{BIO}$ between the average PCA representation of biological label query and reference. Circle size and number inside circles on the bottom row correspond to average pairwise distance $D_{REP}$ between replicates for individual biological labels, weighted by replicates' population sizes. Circle fill color corresponds to the log2 ratio $R$ of $D_{BIO}$ to $D_{REP}$, according to $R=Log_{2}(D_{BIO}/D_{REP})$. Note that while distances are symmetrical for query-reference pairs, $R$ is not due to division by $D_{REP}$.

A negative $R$ (i.e. a red circle) should raise your attention, as this will mean that the specific query group is closer to the query than the query's replicates are spaced from each other on average, indicating that technical variance is stronger than biological variance for these groups. Keep in mind to include your biological context into interpretation of this plot, as certain overlaps between conditions may be expected depending on biological labels.

Leiden clustering (All Slides)

Different clusters found by Leiden clustering are indicated by different colors in the following plot (in UMAP space):

Leiden clustering

Leiden clustering vs condition (All Slides)

The following plot indicates the Leiden cluster (colors) to which each pixels of a specific condition (one row of the plot) has been assigned:

The following plot indicates the condition (colors) to which each pixels of a specific Leiden cluster (one row of the plot) has been assigned:

DE analysis plots (All Slides)

The following plot shows the top 15 molecules that are most significantly differentially expressed between the different Leiden clusters:

UMAP of Differential Expressed markers for Leiden cluster 7-days-cells

The following UMAP plots show the intensities of the top 16 ions that are differentially expressed in Leiden cluster 7-days-cells:

UMAP of Differential Expressed markers for Leiden cluster 14-days-cells

The following UMAP plots show the intensities of the top 16 ions that are differentially expressed in Leiden cluster 14-days-cells:

UMAP of Differential Expressed markers for Leiden cluster Stem-cells

The following UMAP plots show the intensities of the top 16 ions that are differentially expressed in Leiden cluster Stem-cells: